Build-pipeline resilience fixes: BioMart retries, GENCODE streaming, URL updates - #234

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af8 wants to merge 6 commits into

ndaniel:masterfrom

af8:fix/build-resilience-2026-05

Commits on May 25, 2026

Add retry logic to BioMart-based download scripts
af8
committed
52dddbf
Add per-chromosome retry and fail-on-incomplete in get_paralogs and get_exons_positions
af8
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3cedc64
Stream GENCODE GTF decompression to avoid OOM and add FTP retry
af8
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e4a5dd1
Update URLs for migrated and dead resources
af8
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2d7b847
Fix get_synonyms.py filter to exclude GRCh37 entries instead of .gz files
af8
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283d9b5
Auto-pin GENCODE release in fusioncatcher-build.py based on Ensembl version
af8
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4e33ae7